Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI

From: Chuck is Busy <>
Date: Sat, 13 Mar 2021 18:03:08 -0500

So...CHARMM-GUI converts the structure to the Amber format with prmtop and
rst7. I used those files to run my simulation, and I used that same prmtop
file to create my complex, receptor, and ligand prmtop file with cpptraj.
At the time, I didn't realize that my CHARMM-GUI prmtop file doesn't have
any radii defined. After I create my 3 topology files to run sander, I get
that error because none of those files have a radii mentioned. Then I go
back and set mbondi as my radii for my 3 topology files and I guess I'm
overestimating my values.

If my simulation was run without defining a radii, what radii or what
values can I set for my 3 topology files to get reasonable values with
Or can I use cpptraj to trajout a trajectory with new radii?

On Sat, Mar 13, 2021 at 5:08 PM David A Case <> wrote:

> On Sat, Mar 13, 2021, Chuck is Busy wrote:
> >
> >Do you have any better insight on how I can define the 1-4 EEL and 1-4 VDW
> >scale factors so I can run PBSA calculations on my protein system? The
> >protein membrane system was built in CHARMM-GUI and the CHARMM force field
> >but simulated using AMBER.
> If you ran the simulation with Amber, you have prmtop files with the
> appropriate values of SCEE and SCNB in them (as highlighted here from your
> output):
> >| Note: 1-4 EEL scale factors are being read from the topology file.
> >| Note: 1-4 VDW scale factors are being read from the topology file.
> >If I set my radii to mbondi with and set scnb and scee to 1. I
> >can get MMPBSA to run this way using sander, but after doing my
> >subtractions I get extremely positive values like 1200 to 1700. Wondering
> >if there is a more appropriate way to do this..
> Why are you changing scnb and scee with parmed? Setting the radii makes
> sense to me, but I'm not sure why you want to change scnb and scee.
> ...hoping the others on the list will correct any mistakes above.
> ....dac
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Received on Sat Mar 13 2021 - 15:30:02 PST
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